Regulation of allergies across the body by microbial metabolites

Regulation of allergies across the body by microbial metabolites

  • Wu, A. C., Dahlin, A. & Wang, A. L. The role of environmental risk factors on the development of childhood allergic rhinitis. Children 8, 708 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tamagawa-Mineoka, R. & Katoh, N. Atopic Dermatitis: identification and management of complicating factors. Int. J. Mol. Sci. 21, 2671 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nolte, H., Backer, V. & Porsbjerg, C. Environmental factors as a cause for the increase in allergic disease. Ann. Allergy Asthma Immunol. 87, 7–11 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Francis, O. L., Wang, K. Y., Kim, E. H. & Moran, T. P. Common food allergens and cross-reactivity. J. Food Allergy 2, 17–21 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sogkas, G. et al. Cellular and molecular mechanisms breaking immune tolerance in inborn errors of immunity. Cell Mol. Immunol. 18, 1122–1140 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bloom, B., Cohen, R. A. & Freeman, G. Summary health statistics for U.S. children: National Health Interview Survey, 2010. Vital Health Stat. 10, 1–80 (2011).


    Google Scholar
     

  • van de Veen, W., Wirz, O. F., Globinska, A. & Akdis, M. Novel mechanisms in immune tolerance to allergens during natural allergen exposure and allergen-specific immunotherapy. Curr. Opin. Immunol. 48, 74–81 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Ptaschinski, C. & Gibbs, B. F. Early-life risk factors which govern pro-allergic immunity. Semin. Immunopathol 46, 9 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lukacs, N. W. & Hogan, S. P. Food allergy: begin at the skin, end at the mast cell?. Nat. Rev. Immunol. 25, 783–797 (2025).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Molofsky, A. B. & Locksley, R. M. The ins and outs of innate and adaptive type 2 immunity. Immunity 56, 704–722 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cobos-Uribe, C. & Rebuli, M. E. Understanding the functional role of the microbiome and metabolome in asthma. Curr. Allergy Asthma Rep 23, 67–76 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • McGowan, E. C. & Keet, C. A. Prevalence of self-reported food allergy in the National Health and Nutrition Examination Survey (NHANES) 2007–2010. J. Allergy Clin. Immunol. 132, 1216–1219 e1215 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Trompette, A. et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat. Med. 20, 159–166 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yu, R., Yang, B., Cai, L., Lu, X. & Wang, X. Excess free fructose beverages and allergy in children and adolescents: results from NHANES 2005-2006. Ann. Fam. Med. 16, 408–418 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Han, Y. Y. et al. The dietary inflammatory index and current wheeze among children and adults in the United States. J. Allergy Clin. Immunol. Pract. 6, 834–841 e832 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Melo, B., Rezende, L., Machado, P., Gouveia, N. & Levy, R. Associations of ultra-processed food and drink products with asthma and wheezing among Brazilian adolescents. Pediatr. Allergy Immunol. 29, 504–511 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Augustine, T., Kumar, M., Al Khodor, S. & van Panhuys, N. Microbial dysbiosis tunes the immune response towards allergic disease outcomes. Clin. Rev. Allergy Immunol. 65, 43–71 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Penders, J., Stobberingh, E. E., van den Brandt, P. A. & Thijs, C. The role of the intestinal microbiota in the development of atopic disorders. Allergy 62, 1223–1236 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Melli, L. C., do Carmo-Rodrigues, M. S., Araujo-Filho, H. B., Sole, D. & de Morais, M. B. Intestinal microbiota and allergic diseases: a systematic review. Allergol. Immunopathol. 44, 177–188 (2016).

    Article 
    CAS 

    Google Scholar
     

  • Azad, M. B. et al. Infant gut microbiota and the hygiene hypothesis of allergic disease: impact of household pets and siblings on microbiota composition and diversity. Allergy Asthma Clin. Immunol. 9, 15 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, C. H. Immune regulation by microbiome metabolites. Immunology 154, 220–229 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wong, J. M., De Souza, R., Kendall, C. W., Emam, A. & Jenkins, D. J. Colonic health: fermentation and short chain fatty acids. J. Clin. Gastroenterol. 40, 235–243 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Xue, C. et al. Tryptophan metabolism in health and disease. Cell Metab. 35, 1304–1326 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Nuse, B., Holland, T., Rauh, M., Gerlach, R. G. & Mattner, J. L-Arginine metabolism as pivotal interface of mutual host-microbe interactions in the gut. Gut Microbes 15, 2222961 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dodd, D. et al. A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites. Nature 551, 648–652 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sayin, S. amaI. et al. Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist. Cell Metab. 17, 225–235 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Krautkramer, K. A., Fan, J. & Backhed, F. Gut microbial metabolites as multi-kingdom intermediates. Nat. Rev. Microbiol. 19, 77–94 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Takeuchi, T., Nakanishi, Y. & Ohno, H. Microbial metabolites and gut immunology. Annu. Rev. Immunol. 42, 153–178 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kim, M., Qie, Y., Park, J. & Kim, C. H. Gut microbial metabolites fuel host antibody responses. Cell Host Microbe 20, 202–214 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rooks, M. G. & Garrett, W. S. Gut microbiota, metabolites and host immunity. Nat. Rev. Immunol. 16, 341–352 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fahur Bottino, G. et al. Early life microbial succession in the gut follows common patterns in humans across the globe. Nat. Commun. 16, 660 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nathan, A. M. et al. Colonization of the newborn respiratory tract and its association with respiratory morbidity in the first 6 months of life: a prospective cohort study. Int. J. Infect. Dis. 122, 712–720 (2022).

    Article 
    PubMed 

    Google Scholar
     

  • Belkaid, Y. & Hand, T. W. Role of the microbiota in immunity and inflammation. Cell 157, 121–141 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dapa, T. & Xavier, K. B. Effect of diet on the evolution of gut commensal bacteria. Gut Microbes 16, 2369337 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Burger, E. & Gallo, R. L. Host-microbiome interactions in the holobiome of atopic dermatitis. J. Allergy Clin. Immunol. 151, 1236–1238 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sbihi, H. et al. Thinking bigger: How early-life environmental exposures shape the gut microbiome and influence the development of asthma and allergic disease. Allergy 74, 2103–2115 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Capone, K. A., Dowd, S. E., Stamatas, G. N. & Nikolovski, J. Diversity of the human skin microbiome early in life. J. Invest. Dermatol. 131, 2026–2032 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hoskinson, C. et al. Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease. Nat. Commun. 14, 4785 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bunyavanich, S. et al. Early-life gut microbiome composition and milk allergy resolution. J. Allergy Clin. Immunol. 138, 1122–1130 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Durack, J. et al. Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation. Nat. Commun. 9, 707 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, J. E. & Kim, H. S. Microbiome of the skin and gut in atopic dermatitis (AD): understanding the pathophysiology and finding novel management strategies. J. Clin. Med. 8, 444 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nylund, L. et al. Severity of atopic disease inversely correlates with intestinal microbiota diversity and butyrate-producing bacteria. Allergy 70, 241–244 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Goldberg, M. R. et al. Microbial signature in IgE-mediated food allergies. Genome Med. 12, 92 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bunyavanich, S. & Berin, M. C. Food allergy and the microbiome: current understandings and future directions. J. Allergy Clin. Immunol. 144, 1468–1477 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Davis, E. C., Jackson, C. M., Ting, T., Harizaj, A. & Jarvinen, K. M. Predictors and biomarkers of food allergy and sensitization in early childhood. Ann. Allergy Asthma Immunol. 129, 292–300 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • De Filippis, F. et al. Specific gut microbiome signatures and the associated pro-inflamatory functions are linked to pediatric allergy and acquisition of immune tolerance. Nat. Commun. 12, 5958 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Berni Canani, R. et al. Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants. ISME J. 10, 742–750 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Fieten, K. B. et al. Fecal microbiome and food allergy in pediatric atopic dermatitis: a cross-sectional pilot study. Int. Arch. Allergy Immunol. 175, 77–84 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Stefka, A. T. et al. Commensal bacteria protect against food allergen sensitization. Proc. Natl Acad. Sci. USA 111, 13145–13150 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Savage, J. H. et al. A prospective microbiome-wide association study of food sensitization and food allergy in early childhood. Allergy 73, 145–152 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tanaka, M. et al. Signatures in the gut microbiota of Japanese infants who developed food allergies in early childhood. FEMS Microbiol. Ecol. https://doi.org/10.1093/femsec/fix099 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Chen, C. C., Chen, K. J., Kong, M. S., Chang, H. J. & Huang, J. L. Alterations in the gut microbiotas of children with food sensitization in early life. Pediatr. Allergy Immunol. 27, 254–262 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • Bjorksten, B., Naaber, P., Sepp, E. & Mikelsaar, M. The intestinal microflora in allergic Estonian and Swedish 2-year-old children. Clin. Exp. Allergy 29, 342–346 (1999).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bisgaard, H. et al. Reduced diversity of the intestinal microbiota during infancy is associated with increased risk of allergic disease at school age. J. Allergy Clin. Immunol. 128, 646–652 (2011).

    Article 
    PubMed 

    Google Scholar
     

  • Tsilochristou, O. et al. Association of Staphylococcus aureus colonization with food allergy occurs independently of eczema severity. J. Allergy Clin. Immunol. 144, 494–503 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ling, Z. et al. Altered fecal microbiota composition associated with food allergy in infants. Appl. Environ. Microbiol. 80, 2546–2554 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Azad, M. B. et al. Infant gut microbiota and food sensitization: associations in the first year of life. Clin. Exp. Allergy 45, 632–643 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Panzer, A. R. et al. The impact of prenatal dog keeping on infant gut microbiota development. Clin. Exp. Allergy 53, 833–845 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bao, R. et al. Fecal microbiome and metabolome differ in healthy and food-allergic twins. J. Clin. Invest. 131, e141935 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ogata, Y. et al. Complete genome sequence of Phascolarctobacterium faecium JCM 30894, a succinate-utilizing bacterium isolated from human feces. Microbiol. Resour. Announc. 8, e01487–18 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ze, X., Duncan, S. H., Louis, P. & Flint, H. J. Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J. 6, 1535–1543 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wan, J. et al. Alterations in the gut microbiome of young children with airway allergic disease revealed by next-generation sequencing. J. Asthma Allergy 16, 961–972 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, Y. J. & Bunyavanich, S. Microbial influencers: the airway microbiome’s role in asthma. J. Clin. Invest. 135, e184316 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Earl, C. S., An, S. Q. & Ryan, R. P. The changing face of asthma and its relation with microbes. Trends Microbiol. 23, 408–418 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Barcik, W., Boutin, R. C. T., Sokolowska, M. & Finlay, B. B. The role of lung and gut microbiota in the pathology of asthma. Immunity 52, 241–255 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dickson, R. P. & Huffnagle, G. B. The lung microbiome: new principles for respiratory bacteriology in health and disease. PLoS Pathog. 11, e1004923 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Segal, L. N. et al. Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Nat. Microbiol. 1, 16031 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Durack, J. et al. Distinct associations of sputum and oral microbiota with atopic, immunologic, and clinical features in mild asthma. J. Allergy Clin. Immunol. 146, 1016–1026 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vael, C., Nelen, V., Verhulst, S. L., Goossens, H. & Desager, K. N. Early intestinal Bacteroides fragilis colonisation and development of asthma. BMC Pulm. Med. 8, 19 (2008).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Arrieta, M. C. et al. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci. Transl. Med. 7, 307ra152 (2015).

    Article 
    PubMed 

    Google Scholar
     

  • Bisgaard, H. et al. Childhood asthma after bacterial colonization of the airway in neonates. N. Engl. J. Med. 357, 1487–1495 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Liwen, Z., Yu, W., Liang, M., Kaihong, X. & Baojin, C. A low abundance of Bifidobacterium but not Lactobacillius in the feces of Chinese children with wheezing diseases. Medicine 97, e12745 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stiemsma, L. T. et al. Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma. Clin. Sci. 130, 2199–2207 (2016).

    Article 
    CAS 

    Google Scholar
     

  • Lee, S. H., Gong, Y. N. & Ryoo, E. Clostridium difficile colonization and/or infection during infancy and the risk of childhood allergic diseases. Korean J. Pediatr. 60, 145–150 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhou, M. S. et al. Altered diversity and composition of gut microbiota in patients with allergic rhinitis. Microb. Pathog. 161, 105272 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Roduit, C. et al. High levels of butyrate and propionate in early life are associated with protection against atopy. Allergy 74, 799–809 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hu, Q. et al. Tryptophan metabolite-regulated Treg responses contribute to attenuation of airway inflammation during specific immunotherapy in a mouse asthma model. Hum. Vaccin. Immunother. 16, 1891–1899 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • van der Sluijs, K. F. et al. Systemic tryptophan and kynurenine catabolite levels relate to severity of rhinovirus-induced asthma exacerbation: a prospective study with a parallel-group design. Thorax 68, 1122–1130 (2013).

    Article 
    PubMed 

    Google Scholar
     

  • Wu, R. et al. The bile acid-activated retinoic acid response in dendritic cells is involved in food allergen sensitization. Allergy 77, 483–498 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kim, C. H., Park, J. & Kim, M. Gut microbiota-derived short-chain fatty acids, T cells, and inflammation. Immune Netw. 14, 277–288 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, C. H. Control of lymphocyte functions by gut microbiota-derived short-chain fatty acids. Cell Mol. Immunol. 18, 1161–1171 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Brown, A. J. et al. The Orphan G protein-coupled receptors GPR41 and GPR43 are activated by propionate and other short chain carboxylic acids. J. Biol. Chem. 278, 11312–11319 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Nilsson, N. E., Kotarsky, K., Owman, C. & Olde, B. Identification of a free fatty acid receptor, FFA2R, expressed on leukocytes and activated by short-chain fatty acids. Biochem. Biophys. Res. Commun. 303, 1047–1052 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Le Poul, E. et al. Functional characterization of human receptors for short chain fatty acids and their role in polymorphonuclear cell activation. J. Biol. Chem. 278, 25481–25489 (2003).

    Article 
    PubMed 

    Google Scholar
     

  • Cuisset, L., Tichonicky, L. & Delpech, M. A protein phosphatase is involved in the inhibition of histone deacetylation by sodium butyrate. Biochem. Biophys. Res. Commun. 246, 760–764 (1998).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Park, J. et al. Short-chain fatty acids induce both effector and regulatory T cells by suppression of histone deacetylases and regulation of the mTOR–S6K pathway. Mucosal Immunol. 8, 80–93 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kim, M. H., Kang, S. G., Park, J. H., Yanagisawa, M. & Kim, C. H. Short-chain fatty acids activate GPR41 and GPR43 on intestinal epithelial cells to promote inflammatory responses in mice. Gastroenterology 145, 396–406 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sepahi, A., Liu, Q., Friesen, L. & Kim, C. H. Dietary fiber metabolites regulate innate lymphoid cell responses. Mucosal Immunol. 14, 317–330 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chun, E. et al. Metabolite-sensing receptor Ffar2 regulates colonic group 3 innate lymphoid cells and gut immunity. Immunity 51, 871–884 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Thio, C. L., Chi, P. Y., Lai, A. C. & Chang, Y. J. Regulation of type 2 innate lymphoid cell-dependent airway hyperreactivity by butyrate. J. Allergy Clin. Immunol. 142, 1867–1883 e1812 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ticho, A. L., Malhotra, P., Dudeja, P. K., Gill, R. K. & Alrefai, W. A. Bile acid receptors and gastrointestinal functions. Liver Res. 3, 31–39 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fleishman, J. S. & Kumar, S. Bile acid metabolism and signaling in health and disease: molecular mechanisms and therapeutic targets. Signal Transduct. Target. Ther. 9, 97 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Taylor, S. A. & Green, R. M. Bile acids, microbiota, and metabolism. Hepatology 68, 1229–1231 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chiang, J. Y. L. & Ferrell, J. M. Discovery of farnesoid X receptor and its role in bile acid metabolism. Mol. Cell Endocrinol. 548, 111618 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sorrentino, G. et al. Bile acids signal via TGR5 to activate intestinal stem cells and epithelial regeneration. Gastroenterology 159, 956–968 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Thomas, C. et al. TGR5-mediated bile acid sensing controls glucose homeostasis. Cell Metab. 10, 167–177 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Perino, A. et al. TGR5 reduces macrophage migration through mTOR-induced C/EBPbeta differential translation. J. Clin. Invest. 124, 5424–5436 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Qi, Y., Duan, G., Wei, D., Zhao, C. & Ma, Y. The bile acid membrane receptor tgr5 in cancer: friend or foe?. Molecules 27, 5292 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Duboc, H., Tache, Y. & Hofmann, A. F. The bile acid TGR5 membrane receptor: from basic research to clinical application. Dig. Liver Dis. 46, 302–312 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Staudinger, J. L. et al. The nuclear receptor PXR is a lithocholic acid sensor that protects against liver toxicity. Proc. Natl Acad. Sci. USA 98, 3369–3374 (2001).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, R. et al. Conjugated bile acids promote cholangiocarcinoma cell invasive growth through activation of sphingosine 1-phosphate receptor 2. Hepatology 60, 908–918 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, X. J., Chen, B. Y., Yang, B. W., Yue, T. L. & Guo, C. F. Short communication: chemical structure, concentration, and pH are key factors influencing antimicrobial activity of conjugated bile acids against lactobacilli. J. Dairy Sci. 104, 1524–1530 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jia, H., He, X., Jiang, T. & Kong, F. Roles of bile acid-activated receptors in monocytes-macrophages and dendritic cells. Cells 14, 920 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Paik, D. et al. Human gut bacteria produce Tau(Eta)17-modulating bile acid metabolites. Nature 603, 907–912 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Heath-Pagliuso, S. et al. Activation of the Ah receptor by tryptophan and tryptophan metabolites. Biochemistry 37, 11508–11515 (1998).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Negishi, T. et al. Effects of aryl hydrocarbon receptor signaling on the modulation of TH1/TH2 balance. J. Immunol. 175, 7348–7356 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Xuan, M. et al. Polyamines: their significance for maintaining health and contributing to diseases. Cell Commun. Signal 21, 348 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Saha, P. P. et al. Gut microbe-generated phenylacetylglutamine is an endogenous allosteric modulator of beta2-adrenergic receptors. Nat. Commun. 15, 6696 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hu, J. et al. Gut microbiota-derived 3-phenylpropionic acid promotes intestinal epithelial barrier function via AhR signaling. Microbiome 11, 102 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Colosimo, D. A. et al. Mapping interactions of microbial metabolites with human G-protein-coupled receptors. Cell Host Microbe 26, 273–282 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nguyen, A. V. & Soulika, A. M. The dynamics of the skin’s immune system. Int. J. Mol. Sci. 20, 1811 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Luo, C. H. et al. Staphylococcus aureus exacerbates dermal IL-33/ILC2 axis activation through evoking RIPK3/MLKL-mediated necroptosis of dry skin. JCI Insight 9, e166821 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, X. et al. Activation of aryl hydrocarbon receptor in Langerhans cells by a microbial metabolite of tryptophan negatively regulates skin inflammation. J. Dermatol. Sci. 100, 192–200 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lefevre, M. A., Vocanson, M. & Nosbaum, A. Role of tissue-resident memory T cells in the pathophysiology of allergic contact dermatitis. Curr. Opin. Allergy Clin. Immunol. 21, 355–360 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Nestle, F. O., Di Meglio, P., Qin, J. Z. & Nickoloff, B. J. Skin immune sentinels in health and disease. Nat. Rev. Immunol. 9, 679–691 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kumar, S., Jeong, Y., Ashraf, M. U. & Bae, Y. S. Dendritic cell-mediated Th2 immunity and immune disorders. Int. J. Mol. Sci. 20, 2159 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kopf, M., Schneider, C. & Nobs, S. P. The development and function of lung-resident macrophages and dendritic cells. Nat. Immunol. 16, 36–44 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Verma, M., Can, U. I. & Reinhardt, R. L. ILC2 diversity, location, and function in pulmonary disease. Immunol. Rev. 332, e70036 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, C. H., Hashimoto-Hill, S. & Kim, M. Migration and tissue tropism of innate lymphoid cells. Trends Immunol. 37, 68–79 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Drake, L. Y. & Kita, H. Group 2 innate lymphoid cells in the lung. Adv. Immunol. 124, 1–16 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shirley, S. et al. A vasculature-resident innate lymphoid cell population in mouse lungs. Nat. Commun. 16, 3718 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Naderi, W., Schreiner, D. & King, C. G. T-cell–B-cell collaboration in the lung. Curr. Opin. Immunol. 81, 102284 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Macedo, B. G., Masuda, M. Y. & Borges da Silva, H. Location versus ID: what matters to lung-resident memory T cells?. Front. Immunol. 15, 1355910 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bertrand, Y., Sanchez-Montalvo, A., Hox, V., Froidure, A. & Pilette, C. IgA-producing B cells in lung homeostasis and disease. Front. Immunol. 14, 1117749 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Antunes, K. H. et al. Airway-delivered short-chain fatty acid acetate boosts antiviral immunity during rhinovirus infection. J. Allergy Clin. Immunol. 151, 447–457 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Grondin, J. A., Kwon, Y. H., Far, P. M., Haq, S. & Khan, W. I. Mucins in intestinal mucosal defense and inflammation: learning from clinical and experimental studies. Front. Immunol. 11, 2054 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bemark, M., Pitcher, M. J., Dionisi, C. & Spencer, J. Gut-associated lymphoid tissue: a microbiota-driven hub of B cell immunity. Trends Immunol. 45, 211–223 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Diefenbach, A., Gnafakis, S. & Shomrat, O. Innate lymphoid cell–epithelial cell modules sustain intestinal homeostasis. Immunity 52, 452–463 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Stanbery, A. G., Shuchi, S., Jakob von, M., Tait Wojno, E. D. & Ziegler, S. F. TSLP, IL-33, and IL-25: not just for allergy and helminth infection. J. Allergy Clin. Immunol. 150, 1302–1313 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ornelas, A., Dowdell, A. S., Lee, J. S. & Colgan, S. P. Microbial metabolite regulation of epithelial cell-cell interactions and barrier function. Cells 11, 944 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fung, C. et al. Tuft cells mediate commensal remodeling of the small intestinal antimicrobial landscape. Proc. Natl Acad. Sci. USA 120, e2216908120 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Eshleman, E. M. et al. Microbiota-derived butyrate restricts tuft cell differentiation via histone deacetylase 3 to modulate intestinal type 2 immunity. Immunity 57, 319–332 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, H. B. et al. Skin microbiome dynamics in atopic dermatitis: understanding host–microbiome interactions. Allergy Asthma Immunol. Res. 17, 165–180 (2025).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Qiu, Z. et al. A dysregulated sebum-microbial metabolite-IL-33 axis initiates skin inflammation in atopic dermatitis. J. Exp. Med. 219, e20212397 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Trompette, A. et al. Gut-derived short-chain fatty acids modulate skin barrier integrity by promoting keratinocyte metabolism and differentiation. Mucosal Immunol. 15, 908–926 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Trompette, A. et al. Dietary fiber confers protection against flu by shaping Ly6c patrolling monocyte hematopoiesis and CD8+ T cell metabolism. Immunity 48, 992–1005 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wang, Y. et al. A precision microbiome approach using sucrose for selective augmentation of Staphylococcus epidermidis fermentation against Propionibacterium acnes. Int. J. Mol. Sci. 17, 1870 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Leon Carrion, S., Sutter, C. H. & Sutter, T. R. Combined treatment with sodium butyrate and PD153035 enhances keratinocyte differentiation. Exp. Dermatol. 23, 211–214 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Blicharz, L. et al. Severity of atopic dermatitis is associated with gut-derived metabolites and leaky gut-related biomarkers. Sci. Rep. 15, 26146 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yu, J. et al. A tryptophan metabolite of the skin microbiota attenuates inflammation in patients with atopic dermatitis through the aryl hydrocarbon receptor. J. Allergy Clin. Immunol. 143, 2108–2119(2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kang, Y. M. et al. Indole-3-carbinol alleviates allergic skin inflammation via periostin/thymic stromal lymphopoietin suppression in atopic dermatitis. Chin. Med. 19, 177 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jena, P. K. et al. Long-term Western diet intake leads to dysregulated bile acid signaling and dermatitis with Th2 and Th17 pathway features in mice. J. Dermatol. Sci. 95, 13–20 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, E. J. et al. Ursodeoxycholic acid alleviates atopic dermatitis-associated inflammatory responses in HaCaT and RBL-2H3 cells and DNCB/DFE-treated mice. Life Sci. 344, 122560 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lin, D. L. et al. 12,13-diHOME promotes inflammatory macrophages and epigenetically modifies their capacity to respond to microbes and allergens. J. Immunol. Res. 2024, 2506586 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Prescott, S. L. et al. A global survey of changing patterns of food allergy burden in children. World Allergy Organ J. 6, 21 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Valenta, R., Hochwallner, H., Linhart, B. & Pahr, S. Food allergies: the basics. Gastroenterology 148, 1120–1131 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Izadi, N., Luu, M., Ong, P. Y. & Tam, J. S. The role of skin barrier in the pathogenesis of food allergy. Children 2, 382–402 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ferraro, V. A., Zanconato, S. & Carraro, S. The epithelial barrier hypothesis in food allergies: the state of the art. Nutrients 17, 1014 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shi, J. et al. Butyrate alleviates food allergy by improving intestinal barrier integrity through suppressing oxidative stress-mediated Notch signaling. iMeta 4, e70024 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tett, A. et al. The Prevotella copri complex comprises four distinct clades underrepresented in Westernized populations. Cell Host Microbe 26, 666–679 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Larsen, J. M. The immune response to Prevotella bacteria in chronic inflammatory disease. Immunology 151, 363–374 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Scher, J. U. et al. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. eLife 2, e01202 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Folkerts, J. et al. Butyrate inhibits human mast cell activation via epigenetic regulation of FcepsilonRI-mediated signaling. Allergy 75, 1966–1978 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nagata, K. et al. Butyrate, valerate, and niacin ameliorate anaphylaxis by suppressing ige-dependent mast cell activation: roles of GPR109A, PGE2, and epigenetic regulation. J. Immunol. 212, 771–784 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tan, J. et al. Dietary fiber and bacterial SCFA enhance oral tolerance and protect against food allergy through diverse cellular pathways. Cell Rep. 15, 2809–2824 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shao, H. et al. Bifidobacterium breve M-16V alleviates cow’s milk allergy in a mouse model via gut microbiota-derived indole-3-propionic acid-aryl hydrocarbon receptor signaling axis. Allergy https://doi.org/10.1111/all.16684 (2025).

    Article 
    PubMed 

    Google Scholar
     

  • Hammerschmidt-Kamper, C. et al. Indole-3-carbinol, a plant nutrient and AhR-ligand precursor, supports oral tolerance against OVA and improves peanut allergy symptoms in mice. PLoS ONE 12, e0180321 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Song, X. et al. Microbial bile acid metabolites modulate gut RORγ+ regulatory T cell homeostasis. Nature 577, 410–415 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bhaumik, S., Mickael, M. E., Moran, M., Spell, M. & Basu, R. RORgammat promotes Foxp3 expression by antagonizing the effector program in colonic regulatory T cells. J. Immunol. 207, 2027–2038 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ozcam, M. et al. Gut microbial bile and amino acid metabolism associate with peanut oral immunotherapy failure. Nat. Commun. 16, 6330 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lewis, G. et al. Dietary fiber-induced microbial short chain fatty acids suppress ILC2-dependent airway inflammation. Front. Immunol. 10, 2051 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cheng, H. Y. et al. Evaluation of stool short chain fatty acids profiles in the first year of life with childhood atopy-related outcomes. Front. Allergy 3, 873168 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lee-Sarwar, K. A., Lasky-Su, J., Kelly, R. S., Litonjua, A. A. & Weiss, S. T. Gut microbial-derived metabolomics of asthma. Metabolites 10, 97 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chiu, C. Y. et al. Gut microbial-derived butyrate is inversely associated with IgE responses to allergens in childhood asthma. Pediatr. Allergy Immunol. 30, 689–697 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Huang, M. T. et al. Short-chain fatty acids ameliorate allergic airway inflammation via sequential induction of PMN-MDSCs and Treg cells. J. Allergy Clin. Immunol. Glob. 2, 100163 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cait, A. et al. Microbiome-driven allergic lung inflammation is ameliorated by short-chain fatty acids. Mucosal Immunol. 11, 785–795 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Theiler, A. et al. Butyrate ameliorates allergic airway inflammation by limiting eosinophil trafficking and survival. J Allergy Clin. Immunol. 144, 764–776 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zaiss, M. M. et al. The intestinal microbiota contributes to the ability of helminths to modulate allergic inflammation. Immunity 43, 998–1010 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yu, B. et al. Microbiota-derived butyrate alleviates asthma via inhibiting Tfh13-mediated IgE production. Signal Transduct. Target Ther. 10, 181 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hu, W. et al. Both living and dead Faecalibacterium prausnitzii alleviate house dust mite-induced allergic asthma through the modulation of gut microbiota and short-chain fatty acid production. J. Sci. Food Agric. 101, 5563–5573 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chen, Z. et al. Vancomycin-induced gut microbiota dysbiosis aggravates allergic rhinitis in mice by altered short-chain fatty acids. Front. Microbiol. 13, 1002084 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, J., Wen, L., Wang, Y. & Chen, F. Therapeutic effect of histone deacetylase inhibitor, sodium butyrate, on allergic rhinitis in vivo. DNA Cell Biol. 35, 203–208 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Miao, Y. et al. Impaired tryptophan metabolism by type 2 inflammation in epithelium worsening asthma. iScience 27, 109923 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, H. et al. Gut microbiota-derived tryptophan metabolites alleviate allergic asthma inflammation in ovalbumin-induced mice. Foods 13, 1336 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Perdijk, O. et al. Antibiotic-driven dysbiosis in early life disrupts indole-3-propionic acid production and exacerbates allergic airway inflammation in adulthood. Immunity 57, 1939–1954 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kelly, R. S. et al. Plasma metabolite profiles in children with current asthma. Clin. Exp. Allergy 48, 1297–1304 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Manni, M. L. et al. Nitroalkene fatty acids modulate bile acid metabolism and lung function in obese asthma. Sci Rep. 11, 17788 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nakada, E. M. et al. Conjugated bile acids attenuate allergen-induced airway inflammation and hyperresponsiveness by inhibiting UPR transducers. JCI Insight 4, e98101 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hamideh, N. & Wong, L. S. Y. Emerging therapeutics in the management of food allergy. Curr. Probl. Pediatr. Adolesc. Health Care 55, 101732 (2025).

    PubMed 

    Google Scholar
     

  • Park, J., Goergen, C. J., HogenEsch, H. & Kim, C. H. Chronically elevated levels of short-chain fatty acids induce t cell-mediated ureteritis and hydronephrosis. J. Immunol. 196, 2388–2400 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Doron, S. & Snydman, D. R. Risk and safety of probiotics. Clin. Infect. Dis. 60, S129–S134 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wicaksono, D. P., Washio, J., Abiko, Y., Domon, H. & Takahashi, N. Nitrite production from nitrate and its link with lactate metabolism in oral Veillonella spp. Appl. Environ. Microbiol. 86, e01255–20 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lopez-Siles, M., Duncan, S. H., Garcia-Gil, L. J. & Martinez-Medina, M. Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics. ISME J. 11, 841–852 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ottman, N. et al. Genome-scale model and omics analysis of metabolic capacities of akkermansia muciniphila reveal a preferential mucin-degrading lifestyle. Appl. Environ. Microbiol. 83, e01014–e01017 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Oliveira, A. S., Saraiva, L. M. & Carvalho, S. M. Staphylococcus epidermidis biofilms undergo metabolic and matrix remodeling under nitrosative stress. Front. Cell Infect. Microbiol. 13, 1200923 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, X. et al. Transcriptomics and metabolomics reveal the adaption of Akkermansia muciniphila to high mucin by regulating energy homeostasis. Sci. Rep. 11, 9073 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, S. M. & Huang, S. L. The commensal anaerobe Veillonella dispar reprograms its lactate metabolism and short-chain fatty acid production during the stationary phase. Microbiol. Spectr. 11, e0355822 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rios-Covian, D., Salazar, N., Gueimonde, M. & de Los Reyes-Gavilan, C. G. Shaping the metabolism of intestinal bacteroides population through diet to improve human health. Front. Microbiol. 8, 376 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, M. J. et al. Recent findings in Akkermansia muciniphila-regulated metabolism and its role in intestinal diseases. Clin. Nutr. 41, 2333–2344 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Distler, W. & Kroncke, A. The lactate metabolism of the oral bacterium Veillonella from human saliva. Arch. Oral Biol. 26, 657–661 (1981).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Myles, I. A. et al. First-in-human topical microbiome transplantation with Roseomonas mucosa for atopic dermatitis. JCI Insight 3, e120608 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hosseinkhani, F. et al. The contribution of gut bacterial metabolites in the human immune signaling pathway of non-communicable diseases. Gut Microbes 13, 1–22 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sen, A. et al. Comprehensive analysis of metabolites produced by co-cultivation of Bifidobacterium breve MCC1274 with human iPS-derived intestinal epithelial cells. Front. Microbiol. 14, 1155438 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bocchio, F. et al. Compendium of Bifidobacterium-based probiotics: characteristics and therapeutic impact on human diseases. Microbiome Res. Rep. 4, 2 (2025).

    CAS 
    PubMed 

    Google Scholar
     

  • Tang, H., Huang, W. & Yao, Y. F. The metabolites of lactic acid bacteria: classification, biosynthesis and modulation of gut microbiota. Microb. Cell 10, 49–62 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Devika, N. T. & Raman, K. Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models. Sci. Rep. 9, 18222 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Candeliere, F. et al. The metabolism of Leuconostoc genus decoded by comparative genomics. Microorganisms 12, 1487 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fuochi, V. et al. Metabolic characterization of supernatants produced by Lactobacillus spp. with in vitro anti-Legionella activity. Front Microbiol 10, 1403 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ponsetto, P., Sasal, E. M., Mazzoli, R., Valetti, F. & Gilardi, G. The potential of native and engineered Clostridia for biomass biorefining. Front. Bioeng. Biotechnol. 12, 1423935 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, S. M., Hung, J. H., Yen, T. N. & Huang, S. L. Mutualistic interactions of lactate-producing lactobacilli and lactate-utilizing Veillonella dispar: lactate and glutamate cross-feeding for the enhanced growth and short-chain fatty acid production. Microb. Biotechnol. 17, e14484 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zuniga, M., Monedero, V. & Yebra, M. J. Utilization of host-derived glycans by intestinal Lactobacillus and Bifidobacterium species. Front. Microbiol. 9, 1917 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zaplana, T., Miele, S. & Tolonen, A. C. Lachnospiraceae are emerging industrial biocatalysts and biotherapeutics. Front. Bioeng. Biotechnol. 11, 1324396 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Fernandez-Cantos, M. V., Babu, A. F., Hanhineva, K. & Kuipers, O. P. Identification of metabolites produced by six gut commensal Bacteroidales strains using non-targeted LC–MS/MS metabolite profiling. Microbiol. Res. 283, 127700 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Russell, D. A., Ross, R. P., Fitzgerald, G. F. & Stanton, C. Metabolic activities and probiotic potential of bifidobacteria. Int. J. Food Microbiol. 149, 88–105 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Catlett, J. L. et al. Metabolic feedback inhibition influences metabolite secretion by the human gut symbiont Bacteroides thetaiotaomicron. mSystems 5, e00252-20 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Oliphant, K. & Allen-Vercoe, E. Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health. Microbiome 7, 91 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Abdugheni, R. et al. Metabolite profiling of human-originated Lachnospiraceae at the strain level. eMeta 1, e58 (2022).

    CAS 

    Google Scholar